He was chief of the Independent Socialist faction, a group which then mustered sixty members, and edited until 1896 their organ in the press, La Petite République. His programme included the collective ownership of the means of production and the international association of labour. However, when in June 1899 he entered Pierre Waldeck-Rousseau's cabinet of "republican defence" as Minister of Commerce, he limited himself to practical reforms, devoting his attention to the improvement of the merchant marine, to the development of trade, of technical education, of the postal system, and to the amelioration of the conditions of labour. Labour questions were entrusted to a separate department, the Direction du Travail, and the pension and insurance office was also raised to the status of a "direction".

As labour minister, Millerand was responsible for the introduction of a wide range of reforms, including the reduction in the maximum workday from 11 to 10 hours in 1904, the introduction of an 8-hour workday for postal employees, the prescribing of maximum hours and minimum wages for all work undertaken by public authorities, the bringing of workers' representatives into the Conseil supérieur de travail, the establishment of arbitration tribunals and inspectors of labour, and the creation of a labour section inside his Ministry of Commerce to tackle the problem of social insurance.

The introduction of trade union representatives on the Supreme Labour Council, the organisation of local labour councils, and instructions to factory inspectors to put themselves in communication with the councils of the trade unions were valuable concessions to labour. He further secured the rigorous application of earlier laws devised for the protection of the working class. His name was especially associated with a project for the establishment of old age pensions, which became law in 1905. In 1898, he became editor of La Lanterne.

He had not joined his independent socialist colleague, Jean Jaurès, in forming the Parti Socialiste Français in 1902, instead forming the small Independent Socialist Party in 1907 which became the Republican-Socialist Party (PRS) in 1911. His influence with the far left had already declined, for it was said that his departure from the true Marxist tradition had disintegrated the movement. He continued to move to the right, being appointed Prime Minister by the conservative President, Paul Deschanel.

During his time as Prime Minister, a decree of February 1920 introduced the eight-hour day for seamen.

When Deschanel had to resign later that year due to his mental disorder, Millerand emerged as a compromise candidate for President between the Bloc National and the remnants of the Bloc des gauches. Millerand appointed Georges Leygues, a politician with a long career of ministerial office, as Prime Minister and attempted to strengthen the executive powers of the Presidency. This move was resisted in the Chamber of Deputies and the French Senate, and Millerand was forced to appoint a stronger figure, Aristide Briand. Briand's appointment was welcomed by both left and right, although the Socialists and the left wing of the Radical Party did not join his government. However, Millerand dismissed Briand after just a year, and appointed the conservative republican, Raymond Poincaré.

Millerand was accused of favouring conservatives in spite of the traditional neutrality of French Presidents and the composition of the legislature. On 14 July 1922, Millerand escaped an assassination attempt by Gustave Bouvet, a young French anarchist. Two years later, Millerand resigned in the face of growing conflict between the elected legislature and the office of the President, following the victory of the Cartel des Gauches. Gaston Doumergue, who was the president of the Senate at the time, was chosen to replace Millerand.

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